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Merge pull request #284 from avandecreme/fix_infer_units_core_dump
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Fix crash when infering units
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@fbergmann
fbergmann committed Nov 30, 2022
2 parents efc1992 + 8aed7f9 commit 226c867
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Showing 3 changed files with 112 additions and 1 deletion.
26 changes: 26 additions & 0 deletions src/sbml/conversion/test/TestInferUnitsConverter.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -392,6 +392,31 @@ START_TEST (test_infer_localParam_fromReaction)
END_TEST


START_TEST (test_infer_reaction_with_4_params_func_call)
{
string filename(TestDataDirectory);
filename += "inferUnits-4.xml";

SBMLDocument* d = readSBMLFromFile(filename.c_str());

fail_unless(d != NULL);

SBMLInferUnitsConverter * units = new SBMLInferUnitsConverter();

units->setDocument(d);

fail_unless (units->convert() == LIBSBML_OPERATION_SUCCESS);

// TO DO infer units using the function formula
// fail_unless(d->getModel()->getParameter("k1")->isSetUnits() == true);
// fail_unless(d->getModel()->getParameter("k1")->getUnits() == "unitSid_0");

delete units;
delete d;
}
END_TEST


Suite *
create_suite_TestInferUnitsConverter (void)
{
Expand All @@ -409,6 +434,7 @@ create_suite_TestInferUnitsConverter (void)
tcase_add_test(tcase, test_infer_baseUnit_fromMath);
tcase_add_test(tcase, test_infer_fromReaction);
tcase_add_test(tcase, test_infer_localParam_fromReaction);
tcase_add_test(tcase, test_infer_reaction_with_4_params_func_call);

suite_add_tcase(suite, tcase);

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82 changes: 82 additions & 0 deletions src/sbml/conversion/test/test-data/inferUnits-4.xml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,82 @@
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" metaid="ea71b239_15b6_4fa3_a76f_dd6c414eede6" version="4">
<model id="MODEL1212210000" metaid="f4425bc4_80db_4c1c_b889_aae600e0ce20" name="Smith2013 - Regulation of Insulin Signalling by Oxidative Stress">
<listOfFunctionDefinitions>
<functionDefinition id="function_1" metaid="_0b927bb6_7666_4bab_9a62_1bb488a2950b" name="Function for R1f_1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar>
<ci> InR </ci>
</bvar>
<bvar>
<ci> Ins </ci>
</bvar>
<bvar>
<ci> cellsurface </ci>
</bvar>
<bvar>
<ci> extracellular </ci>
</bvar>
<bvar>
<ci> k1 </ci>
</bvar>
<apply>
<times/>
<ci> k1 </ci>
<ci> Ins </ci>
<ci> extracellular </ci>
<ci> InR </ci>
<ci> cellsurface </ci>
</apply>
</lambda>
</math>
</functionDefinition>
</listOfFunctionDefinitions>
<listOfCompartments>
<compartment constant="true" id="extracellular" metaid="_33c764a6_3a3f_4ef0_8617_010e61aaadc6" name="extracellular" sboTerm="SBO:0000290" size="8.3E-12" spatialDimensions="3">
</compartment>
<compartment constant="true" id="cellsurface" metaid="_3998f93a_7adc_4437_90cb_86503740c79e" name="cellsurface" outside="extracellular" sboTerm="SBO:0000290" size="6.4E-14" spatialDimensions="3">
</compartment>
<compartment constant="true" id="cytoplasm" metaid="_546b89ee_5e8b_4791_875c_73de58897f5e" name="cytoplasm" outside="cellsurface" sboTerm="SBO:0000290" size="1.65E-11" spatialDimensions="3">
</compartment>
</listOfCompartments>
<listOfSpecies>
<species boundaryCondition="true" compartment="extracellular" constant="true" hasOnlySubstanceUnits="false" id="Ins" initialAmount="0" metaid="_820723ff_e05b_49d4_b9bd_b025befd02dc" name="Ins">
</species>
<species boundaryCondition="false" compartment="cellsurface" constant="false" hasOnlySubstanceUnits="false" id="InR" initialAmount="90000" metaid="d8602ba9_77a8_4307_ab2d_280bbcc14b67" name="InR">
</species>
<species boundaryCondition="false" compartment="cellsurface" constant="false" hasOnlySubstanceUnits="false" id="Ins_InR" initialAmount="0" metaid="_9672349d_f3af_4c17_8def_526d82171d04" name="Ins_InR">
</species>
</listOfSpecies>
<listOfParameters>
<parameter constant="true" id="k1" metaid="_2ad1244a_ce86_42ed_9222_df283a1c56a5" name="k1" value="2E-5"/>
</listOfParameters>
<listOfReactions>
<reaction id="R1f" metaid="b644817b_aa91_4732_9b17_f83803035b63" name="R1f" reversible="false">
<listOfReactants>
<speciesReference metaid="_652747b2_354c_407c_9dee_9680991fa150" species="Ins" stoichiometry="1"/>
<speciesReference metaid="_725a5142_9442_4c37_908f_aeea73cdae7d" species="InR" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="cc7fe296_cb4a_401f_ac8c_64cedf7f36d2" species="Ins_InR" stoichiometry="1"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference metaid="_0d4998c7_4bc9_4fa7_85b8_9fa7250d6151" species="InR"/>
<modifierSpeciesReference metaid="a8a2b586_05fe_478f_a9e7_66a5ff911afe" species="Ins"/>
</listOfModifiers>
<kineticLaw metaid="_1d9b134e_3620_4ad0_8872_400169c862ca">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<ci> function_1 </ci>
<ci> InR </ci>
<ci> Ins </ci>
<ci> cellsurface </ci>
<ci> extracellular </ci>
<ci> k1 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
5 changes: 4 additions & 1 deletion src/sbml/units/UnitFormulaFormatter.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -377,7 +377,10 @@ UnitFormulaFormatter::getUnitDefinitionFromFunction(const ASTNode * node,

if(node->getType() == AST_FUNCTION)
{
const FunctionDefinition *fd =
// The function name get lost by ASTNode::reduceToBinary when it has more
// than one parameter. So we need to check we have a name before calling
// model->getFunctionDefinition to avoid crashing.
const FunctionDefinition *fd = node->getName() == NULL ? NULL :
model->getFunctionDefinition(node->getName());
if (fd && fd->isSetMath())
{
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